DISCUSSION of Rosetta@home Journal (2)

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catalin

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Message 20243 - Posted: 15 Jul 2006, 12:25:05 UTC - in response to Message 20196.  

Your computer is overcommitted, so it went into earliest deadline first (edf) mode. It stops getting new work until it thinks it can handle them all before their deadlines hit. If you want to work on rosetta, pause the climate model for a couple seconds, it will download rosetta wu's, then restart the climate model and it'll do them both.


It works just fine now, thanks!
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Profile Keith E. Laidig
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Message 20248 - Posted: 15 Jul 2006, 14:10:10 UTC - in response to Message 20206.  
Last modified: 15 Jul 2006, 14:10:25 UTC

Might I suggest copying Dr. Baker's post into the project homepage news area? These all get copied and shown on Boincstats where other folks might see it and be interested.

Good idea. It's done. -KEL

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Jeff Gilchrist

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Message 21161 - Posted: 25 Jul 2006, 20:03:52 UTC
Last modified: 25 Jul 2006, 20:04:55 UTC

Not sure if this will be useful to your research but might find it interesting anyways:
http://www.nytimes.com/2006/07/25/science/25dna.html?ex=1311480000&en=34d8e6ced8d42f47&ei=5089&partner=rssyahoo&emc=rss

"Researchers believe they have found a second code in DNA in addition to the genetic code. The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself."

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Profile rbpeake

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Message 23529 - Posted: 19 Aug 2006, 18:55:51 UTC
Last modified: 19 Aug 2006, 18:56:16 UTC

Yes, some excerpts from the Grid Computing conference would be very interesting and much appreciated! :)
Regards,
Bob P.
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BennyRop

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Message 23535 - Posted: 19 Aug 2006, 19:19:07 UTC

we will NOT be backdating credit totals

David: I take this to mean that the data that is used by the stats sites are not going to be updated. But for comparison purposes, will it be done and then show the results for a 24/7 machine running the standard client since Feb in the following setups: A Mac with a decent cpu; An Athlon 64 3000+ running Windows; An Athlon 64 3000+ running Linux; An Intel P4 3.0 Ghz cpu running Windows; An Intel P4 3.0 Ghz cpu running Linux. Showing the credit granted with the old system and the credit granted with the new system.

The purpose being to show that the new system does indeed balance out over time, - i.e. gets over the highs and lows being reported with people using smaller WU run times - and to show that the Linux vs Windows and P4 vs Athlon 64 issues are eliminated (linux/windows parity) or much closer than the current benchmarks suggest (P4 vs Athlon 64)




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DCManiak

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Message 23538 - Posted: 19 Aug 2006, 19:33:06 UTC

we will NOT be backdating credit totals


Good move, doesn't get any simpler put than that.

Of course, I'm sure some will try to limit what that means or interpret it differently.
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hugothehermit

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Message 23623 - Posted: 20 Aug 2006, 5:50:41 UTC
Last modified: 20 Aug 2006, 6:23:41 UTC

We now have computationally designed amino acid sequences for 15 potential vaccine candidates, and we will start the process of making them next tuesday; the first step is to synthesize genes which encode these proteins.


I didn't see any WU's for them? Did I miss them, did you do them on your own computers or did you have them hanging around waiting for some funding?

Exciting stuff indeed!

I know what a catalyst is, but I can't picture what this would do in someone, because you would need to utilise something spare (chemical/protein etc..)within the body with the bad guy wouldn't you?

To all the R@H team and it's mods: As for the credit stuff, don't lose too much sleep over it, I joined BOINC in 2002-06-15 (according to BOINC-stats) and was a seti@home (now called seti@home classic) before that, it's just growing pains, I've seen this happen before and will see it happen again, do your best and don't pull out too much hair :)

Edit: I left out an 'and', then fluffed my bbcode for the edit :)
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riptide
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Message 23680 - Posted: 20 Aug 2006, 13:02:46 UTC - in response to Message 23535.  

[quote]we will NOT be backdating credit totals

I think this is a great idea and a good move.
I love Mr. Smith. He keeps us safe from Alien Scum. He's probably good a Rosetta too.
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Profile Saenger
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Message 23690 - Posted: 20 Aug 2006, 13:27:07 UTC

DB wrote:
Second, To answer a question which came up on the boards--we will NOT be backdating credit totals. The new system will go into place early next week, adding on to the current totals.

That's probably the easiest solution now, but it will leave the stats up to now as they are: a couple of more or less random numbers.

If the possibility of correcting the stats has not been mentioned at all, I would probably be totally happy now, but with the knowledge of this opportunity lost, there's a small tear in my eye.

But go on with the good scientific work, over time the credits issue will sort itself, and the artificial inflated numbers won't make any difference any more.
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doc :)

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Message 23838 - Posted: 20 Aug 2006, 18:28:53 UTC

if its not too much effort could we at least be told how much different (if theres much at all) the rosetta totals, nothing team/user/host specific would be?
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Tom Philippart
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Message 23917 - Posted: 20 Aug 2006, 22:01:40 UTC - in response to Message 23680.  

[quote]we will NOT be backdating credit totals

I think this is a great idea and a good move.

i agree!
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Morphy375
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Message 23937 - Posted: 20 Aug 2006, 23:00:54 UTC - in response to Message 23917.  

[quote]we will NOT be backdating credit totals

I think this is a great idea and a good move.

i agree!


I disagree! And now? ;-))

Teddies....
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FluffyChicken
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Message 24605 - Posted: 24 Aug 2006, 8:53:50 UTC

COuld we have a Journal (3) thread new moderators, So som eof this older (2 to 3 month old) talk can be stored away.

And some new talk about the recent HIV testing etc can be done.
Team mauisun.org
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R.L. Casey

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Message 24662 - Posted: 24 Aug 2006, 10:59:06 UTC - in response to Message 24605.  

Today was an exciting day for the group! ... The next step is to make a gene--a piece of DNA--that codes for the amino acid sequence... we can buy genes for any amino acid sequence for not to much from DNA synthesis companies, and ... Codon ... can make them for us quite cheaply. Today we ordered genes for 16 potential HIV vaccines, 15 potential new enzymes, and 4 potential new protien-protein complexes... Once we have the purified designed proteins, we can see whether they bind the desired antibodies in the case of the vaccine designs or catalyze the desired reactions in the case of the enzymes... hopefully [we will] have crated proteins that can have a very positive effect on the world!


WOW! My first reaction to this post was that I must have inadvertantly come across a futuristic science-fiction thread. It's quite stunning to realize that this kind of science is being done today. Exciting times! Go, Baker Lab!
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BennyRop

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Message 26768 - Posted: 14 Sep 2006, 17:58:23 UTC

For the Casp7 prediction that was shown, it has a number of what seems like different colored 1 inch wide flat ribbons that look like they've been wrapped around a 1 inch diameter copper pipe. They retain the 1 inch diameter of the pipe. Our prediction has a couple of these flat ribbon springs that have an extra spin. Instead of spinning around twice, ours has 3 spins. Instead of 4 spins, ours has five. What's the significance of the number of spins around the copper pipe for these flat ribbons? (How soon can we train Rosetta to count?)


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tralala

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Message 26772 - Posted: 14 Sep 2006, 19:33:24 UTC

Any chance we see a close-to atomic-level resolution prediction like for CASP6 T281 with about 1.5-Å RMSD?
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David Baker
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Message 26792 - Posted: 15 Sep 2006, 0:03:05 UTC - in response to Message 26772.  

Any chance we see a close-to atomic-level resolution prediction like for CASP6 T281 with about 1.5-Å RMSD?



yes--in the next post in a few days
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tralala

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Message 26805 - Posted: 15 Sep 2006, 7:23:47 UTC - in response to Message 26792.  

Any chance we see a close-to atomic-level resolution prediction like for CASP6 T281 with about 1.5-Å RMSD?



yes--in the next post in a few days


Yippie!!! :-)
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Profile proxima

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Message 27275 - Posted: 18 Sep 2006, 10:15:24 UTC

Can we expect a stream of similar "top participants" updates now, as the other CASP7 results come in? Seeing how close we are (or aren't) to each target is even more motivating than the stats, in my opinion (especially when we're as close as that first one looks!)
Alver Valley Software Ltd - Contributing ALL our spare computing power to BOINC, 24x365.
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Message 27520 - Posted: 19 Sep 2006, 6:43:11 UTC
Last modified: 19 Sep 2006, 6:44:05 UTC

RE: the new moderator introductions
I am delighted to thank the four new moderators who are taking care of the rosetta@home message boards--they are doing a great job!

I guess Dr. Baker hasn't visited the NC forum lately, to see the mess his new mods have made.
Nemesis n. A righteous infliction of retribution manifested by an appropriate agent.


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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2)



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